Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain.
Genetics. 2010 Apr;184(4):1133-9. doi: 10.1534/genetics.109.113423. Epub 2010 Feb 1.
While a variety of methods exist to reconstruct ancestral sequences, all of them assume that a single phylogeny underlies all the positions in the alignment and therefore that recombination has not taken place. Using computer simulations we show that recombination can severely bias ancestral sequence reconstruction (ASR), and quantify this effect. If recombination is ignored, the ancestral sequences recovered can be quite distinct from the grand most recent common ancestor (GMRCA) of the sample and better resemble the concatenate of partial most recent common ancestors (MRCAs) at each recombination fragment. When independent phylogenetic trees are assumed for the different recombinant segments, the estimation of the fragment MRCAs improves significantly. Importantly, we show that recombination can change the biological predictions derived from ASRs carried out with real data. Given that recombination is widespread on nuclear genes and in particular in RNA viruses and some bacteria, the reconstruction of ancestral sequences in these cases should consider the potential impact of recombination and ideally be carried out using approaches that accommodate recombination.
虽然存在多种方法可以重建祖先序列，但它们都假设在比对中的所有位置都存在一个单一的系统发育树，因此没有发生重组。通过计算机模拟，我们表明重组可能严重偏置祖先序列重建（ASR），并量化这种影响。如果忽略重组，重建的祖先序列可能与样本的最接近共同祖先（GMRCA）有很大的不同，并且更类似于每个重组片段的部分最近共同祖先（MRCAs）的串联。当为不同的重组片段假设独立的系统发育树时，对片段 MRCAs 的估计会显著改善。重要的是，我们表明重组可以改变从用真实数据进行的 ASR 得出的生物学预测。鉴于重组在核基因中广泛存在，特别是在 RNA 病毒和一些细菌中，在这些情况下重建祖先序列应该考虑重组的潜在影响，理想情况下使用能够适应重组的方法来进行。
